1
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Boxman ILA, Molin R, Persson S, Juréus A, Jansen CCC, Sosef NP, Le Guyader SF, Ollivier J, Summa M, Hautaniemi M, Suffredini E, Di Pasquale S, Myrmel M, Khatri M, Jamnikar-Ciglenecki U, Kusar D, Moor D, Butticaz L, Lowther JA, Walker DI, Stapleton T, Simonsson M, Dirks RAM. An international inter-laboratory study to compare digital PCR with ISO standardized qPCR assays for the detection of norovirus GI and GII in oyster tissue. Food Microbiol 2024; 120:104478. [PMID: 38431324 DOI: 10.1016/j.fm.2024.104478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 03/05/2024]
Abstract
An optimized digital RT-PCR (RT-dPCR) assay for the detection of human norovirus GI and GII RNA was compared with ISO 15216-conform quantitative real-time RT-PCR (RT-qPCR) assays in an interlaboratory study (ILS) among eight laboratories. A duplex GI/GII RT-dPCR assay, based on the ISO 15216-oligonucleotides, was used on a Bio-Rad QX200 platform by six laboratories. Adapted assays for Qiagen Qiacuity or ThermoFisher QuantStudio 3D were used by one laboratory each. The ILS comprised quantification of norovirus RNA in the absence of matrix and in oyster tissue samples. On average, results of the RT-dPCR assays were very similar to those obtained by RT-qPCR assays. The coefficient of variation (CV%) of norovirus GI results was, however, much lower for RT-dPCR than for RT-qPCR in intra-laboratory replicates (eight runs) and between the eight laboratories. The CV% of norovirus GII results was in the same range for both detection formats. Had in-house prepared dsDNA standards been used, the CV% of norovirus GII could have been in favor of the RT-dPCR assay. The ratio between RT-dPCR and RT-qPCR results varied per laboratory, despite using the distributed RT-qPCR dsDNA standards. The study indicates that the RT-dPCR assay is likely to increase uniformity of quantitative results between laboratories.
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Affiliation(s)
- Ingeborg L A Boxman
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Ramia Molin
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Sofia Persson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Anna Juréus
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Claudia C C Jansen
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Nils P Sosef
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Soizick F Le Guyader
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | - Joanna Ollivier
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | | | | | - Elisabetta Suffredini
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Simona Di Pasquale
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Mette Myrmel
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Mamata Khatri
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Urska Jamnikar-Ciglenecki
- University of Ljubljana Veterinary Faculty, Institute of Food Safety, Feed and Environment, Ljubljana, Slovenia.
| | - Darja Kusar
- University of Ljubljana Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia.
| | - Dominik Moor
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - Lisa Butticaz
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - James A Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Tina Stapleton
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Magnus Simonsson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - René A M Dirks
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
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2
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Bogožalec Košir A, Muller S, Žel J, Milavec M, Mallory AC, Dobnik D. Fast and Accurate Multiplex Identification and Quantification of Seven Genetically Modified Soybean Lines Using Six-Color Digital PCR. Foods 2023; 12:4156. [PMID: 38002213 PMCID: PMC10670894 DOI: 10.3390/foods12224156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The proliferation of genetically modified organisms (GMOs) presents challenges to GMO testing laboratories and policymakers. Traditional methods, like quantitative real-time PCR (qPCR), face limitations in quantifying the increasing number of GMOs in a single sample. Digital PCR (dPCR), specifically multiplexing, offers a solution by enabling simultaneous quantification of multiple GMO targets. This study explores the use of the Naica six-color Crystal dPCR platform for quantifying five GM soybean lines within a single six-plex assay. Two four-color assays were also developed for added flexibility. These assays demonstrated high specificity, sensitivity (limit of detection or LOD < 25 copies per reaction) and precision (bias to an estimated copy number concentration <15%). Additionally, two approaches for the optimization of data analysis were implemented. By applying a limit-of-blank (LOB) correction, the limit of quantification (LOQ) and LOD could be more precisely determined. Pooling of reactions additionally lowered the LOD, with a two- to eight-fold increase in sensitivity. Real-life samples from routine testing were used to confirm the assays' applicability for quantifying GM soybean lines in complex samples. This study showcases the potential of the six-color Crystal dPCR platform to revolutionize GMO testing, facilitating comprehensive analysis of GMOs in complex samples.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Sabine Muller
- Stilla Technologies, Biopark 1, Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Allison C. Mallory
- Stilla Technologies, Biopark 1, Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
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3
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Du Y, Chen F, Liu K, Chen C. Effect of Soybean Protein Concentrate Preparation on Copy Numbers and Structural Characteristics of DNA from Genetically Modified Soybean. Foods 2023; 12:foods12102031. [PMID: 37238848 DOI: 10.3390/foods12102031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/01/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
To regulate the degradation of transgenic DNA and lay theoretical foundations for the rational utilization of genetically modified (GM) products, variations in copy numbers and structural characteristics of DNA from GM soybean event GTS 40-3-2 during soybean protein concentrate (SPC) preparation were evaluated. Results showed that defatting and the first ethanol extraction were key procedures inducing DNA degradation. After these two procedures, copy numbers of the lectin and cp4 epsps targets decreased by more than 4 × 108, occupying 36.88-49.30% of the total copy numbers from raw soybean. Atomic force microscopy images visually revealed the degradation of DNA that thinned and shortened during SPC preparation. Circular dichroism spectra suggested a lower helicity of DNA from defatted soybean kernel flour and a conformation transition of DNA from B-type to A-type after ethanol extraction. The fluorescence intensity of DNA decreased during SPC preparation, verifying the DNA damage along this preparation chain.
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Affiliation(s)
- Yan Du
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- National Engineering Research Center of Wheat and Corn Further Processing, Henan University of Technology, Zhengzhou 450001, China
| | - Fusheng Chen
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Kunlun Liu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Chen Chen
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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4
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Wang J, Wang Y, Hu X, Yang Q, Chen Y, Jiang W, Liu X, Liu H, Zeng H. The development of RPA and CRISPR-Cas12a based immunoassay strip for sensitive detection of genetically modified crops. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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5
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International co-validation on absolute quantification of single nucleotide variants of KRAS by digital PCR. Anal Bioanal Chem 2022; 414:5899-5906. [DOI: 10.1007/s00216-022-04155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/01/2022]
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6
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Fraiture MA, Guiderdoni E, Meunier AC, Papazova N, Roosens NH. ddPCR strategy to detect a gene-edited plant carrying a single variation point: Technical feasibility and interpretation issues. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Karppinen K, Avetisyan A, Hykkerud AL, Jaakola L. A dPCR Method for Quantitative Authentication of Wild Lingonberry ( Vaccinium vitis-idaea) versus Cultivated American Cranberry ( V. macrocarpon). Foods 2022; 11:1476. [PMID: 35627046 PMCID: PMC9141823 DOI: 10.3390/foods11101476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Berries of the genus Vaccinium are highly valued health-beneficial superfoods, which are commonly subjected to adulteration and mixed with each other, or with other common berry species. A quantitative DNA-based method utilizing a chip-based digital polymerase chain reaction (dPCR) technique was developed for identifying and quantifying wild lingonberry (V. vitis-idaea) and cultivated American cranberry (V. macrocarpon). The dPCR method with species-specific primers for mini-barcoding was designed based on the indel regions found in the trnI-CAU-trnL-CAA locus in the chloroplast genome. The designed primers were able to amplify only target species, enabling to distinguish the two closely related species with good sensitivity. Our results illustrated the ability of the method to identify lingonberry and American cranberry DNA using PCR without the need for probes or further sequencing. The dPCR method could also quantify the DNA copy number in mixed samples. Based on this study, the method provides a basis for a simple, fast, and sensitive quantitative authentication analysis of lingonberry and American cranberry by dPCR. Moreover, it can also provide a platform for authentication analyses of other plant species as well by utilizing the indel regions of chloroplast genomes.
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Affiliation(s)
- Katja Karppinen
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
| | - Anna Avetisyan
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
| | - Anne Linn Hykkerud
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
| | - Laura Jaakola
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
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8
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Gatto F, Savini C, Sacco MG, Vinciguerra D, Buttinger G, Corbisier P, Mazzara M, Emons H. Single and multi-laboratory validation of a droplet digital PCR method. Food Control 2022; 140:109117. [PMID: 36193189 PMCID: PMC9231119 DOI: 10.1016/j.foodcont.2022.109117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/30/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022]
Abstract
The authorisation of genetically modified food and feed in the EU is subject to the provision of evidence of safety and of the availability of reliable analytical methods. These methods represent an essential tool for official laboratories to enforce a harmonised market control. Here the validation of droplet digital PCR (dPCR) methods has been performed for studying if the performance and acceptance parameters set by EU and other international guidelines for the analysis of genetically modified organisms (GMO) in food and feed are suitable and achievable also with such methods. The single-laboratory validation study showed that performance requirements set for GMO analysis by real time PCR can also be used to assess dPCR-based methods. Moreover, trueness and precision were assessed for both simplex and duplex formats in a multi-laboratory validation study organised according to international standards. Overall, the data on trueness, repeatability and reproducibility precision resulting from the collaborative study are satisfying the acceptance criteria for the respective parameters as stipulated in the EU and other international guidance such as the Codex Committee on Methods of Analysis and Sampling (CCMAS). For instance, the duplex droplet dPCR method for MON810 showed relative repeatability standard deviations from 1.8% to 15.7%, while the relative reproducibility standard deviation was found to be between 2.1% and 16.5% over the dynamic range studied. Moreover, the relative bias of the dPCR methods was well below 25% across the entire dynamic range. In addition, other aspects supporting the application of digital PCR for the control of GMOs on the market were experimentally assessed such as the conversion of the measurement results from copy number ratio to mass fraction, the influence of the DNA extraction step and of the ingredient content. It was found that the DNA extraction step added only a limited contribution to the variability of the measurement results under the studied conditions. The decreasing amount of the target ingredient content may decrease the level of precision of the method, although within the acceptance range of GMO performance parameters. In-house and collaborative validation studies of a droplet digital PCR method. Trueness and precision assessed and compared for simplex and duplex formats in a collaborative study. Evaluation of the influence of DNA extraction and ingredient content. Description of compliance to EU and other international performance requirements for GMO analysis methods. Application of conversion of measurement results from copy number ratios to mass fractions.
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Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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10
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Li J, Gao H, Li Y, Xiao F, Zhai S, Wu G, Wu Y. Event-specific PCR methods to quantify the genetically modified DBN9936 maize. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Temisak S, Thangsunan P, Boonnil J, Yenchum W, Hongthong K, Oss Boll H, Yata T, Rios‐Solis L, Morris P. Accurate determination of meat mass fractions using DNA measurements for quantifying meat adulteration by digital PCR. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Sasithon Temisak
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Pattanapong Thangsunan
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Jiranun Boonnil
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Watiporn Yenchum
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Kanjana Hongthong
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Heloísa Oss Boll
- Department of Genetics and Morphology Institute of Biological Sciences University of Brasília Brasília Federal District Brazil
- Institute for Bioengineering School of Engineering University of Edinburgh Kings Buildings Edinburgh UK
- Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Kings Buildings Edinburgh UK
| | - Teerapong Yata
- Faculty of Veterinary Science Chulalongkorn University Bangkok Thailand
| | - Leonardo Rios‐Solis
- Institute for Bioengineering School of Engineering University of Edinburgh Kings Buildings Edinburgh UK
- Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Kings Buildings Edinburgh UK
| | - Phattaraporn Morris
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
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Morcia C, Bergami R, Scaramagli S, Delogu C, Andreani L, Carnevali P, Tumino G, Ghizzoni R, Terzi V. A Digital PCR Assay to Quantify the Percentages of Hulled vs. Hulless Wheat in Flours and Flour-Based Products. BIOLOGY 2021; 10:biology10111138. [PMID: 34827131 PMCID: PMC8614899 DOI: 10.3390/biology10111138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Several food products, made from hulled wheats, are now offered by the market, ranging from grains and pasta to flour and bakery products. The possibility of verifying the authenticity of wheat species used at any point in the production chain is relevant, in defense of both producers and consumers. A chip digital PCR assay has been developed to detect and quantify percentages of hulless (i.e., common and durum wheat) and hulled (i.e., einkorn, emmer and spelt) wheats in grains, flours and food products. The assay has been designed on a polymorphism in the miRNA172 target site of the AP2-5 transcription factor localized on chromosome 5A and involved in wheat spike morphogenesis and grain threshability. The assay has been evaluated even in a real-time PCR system to assess its applicability and to compare the analytical costs between dPCR and real-time PCR approaches.
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Affiliation(s)
- Caterina Morcia
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy; (C.M.); (R.G.)
| | - Raffaella Bergami
- Coop Italia, Via del Lavoro, 6/8, I-40033 Casalecchio di Reno, BO, Italy; (R.B.); (S.S.)
| | - Sonia Scaramagli
- Coop Italia, Via del Lavoro, 6/8, I-40033 Casalecchio di Reno, BO, Italy; (R.B.); (S.S.)
| | - Chiara Delogu
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Difesa e Certificazione (CREA-DC), Via Emilia km 307, 26838 Tavazzano, LO, Italy; (C.D.); (L.A.)
| | - Lorella Andreani
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Difesa e Certificazione (CREA-DC), Via Emilia km 307, 26838 Tavazzano, LO, Italy; (C.D.); (L.A.)
| | | | - Giorgio Tumino
- Plant Breeding, Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
| | - Roberta Ghizzoni
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy; (C.M.); (R.G.)
| | - Valeria Terzi
- Consiglio Per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy; (C.M.); (R.G.)
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13
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Long L, Yan W, He Y, Dong L, Xing Z, Li C, Xia W, Li F. Development of a Duplex Digital PCR Method to Quantify Five Genetically Modified Soybean Events. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02104-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Long L, Yan W, Li C, Dong L, Liu N, Xing Z, Li F. Event-specific quantitative polymerase chain reaction methods for detection of double-herbicide-resistant genetically modified corn MON 87419 based on the 3'-junction of the insertion site. Biosci Biotechnol Biochem 2021; 85:1468-1475. [PMID: 33720312 DOI: 10.1093/bbb/zbab040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/03/2021] [Indexed: 11/13/2022]
Abstract
MON 87419 was one of the new transgenic corn events developed in US with the trait of herbicide resistance to both dicamba and glyphosate. To monitor unintended release of genetically modified organism in the future, as well as to meet GM-labeling requirements, it is requisite to develop a reliable method for the detection and quantification of MON 87419, an event-specific primer pair was designed to amplify the 3'-junction site between the endogenous genome sequence and the transferred DNA of GM event MON 87419, amplicons of desired size were produced by qualitative polymerase chain reaction (PCR) assay. For the validation of this quantitative method, the mixed samples containing 10%, 1%, and 0.1% MON 87419 ingredient were quantified. The precisions were expressed as relative standard deviations, deviated by 7.87%, 12.94%, and 19.98%, respectively. These results clearly demonstrate that the PCR methods we developed herein can be used for event-specific quantitative testing of the double-herbicide-resistant corn MON 87419.
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Affiliation(s)
- Likun Long
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wei Yan
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Congcong Li
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Liming Dong
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Na Liu
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhenjuan Xing
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Feiwu Li
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
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15
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Yang L, Chen Y, Li R, Xu W, Cui J, Zhang D, Zhang X. Universal LNA Probe-Mediated Multiplex Droplet Digital Polymerase Chain Reaction for Ultrasensitive and Accurate Quantitative Analysis of Genetically Modified Organisms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1705-1713. [PMID: 33528262 DOI: 10.1021/acs.jafc.0c06433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Multiplex and high-throughput assays are becoming the main trends in the development of new nucleic acid detection and quantification methods, such as those for genetically modified organism (GMO) analysis. Here, we report a novel universal LNA probe-mediated droplet digital polymerase chain reaction (PCR) method (ULNA-ddPCR) for multiple DNA target quantification in GMOs. In ULNA-ddPCR, only one universal LNA probe is used for multiple DNA targets instead of using one to one TaqMan probe. The specificity, sensitivity, dynamic range, and accuracy of the ULNA-ddPCR method are determined by employing GM rice analysis as an example. Simplex and triplex ULNA-ddPCR assays for three GM rice events, T2A-1, T1C-19, and G6H1, are established and evaluated. All results indicate that the developed simplex and triplex ULNA-ddPCR assays are suitable for quantitative analysis of GM rice events with high sensitivity, accuracy, and low cost. The ULNA-ddPCR method also has the potential for multiple DNA target quantification in other research fields.
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Affiliation(s)
- Litao Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Yi Chen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenting Xu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjie Cui
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiujie Zhang
- Development Center of Science and Technology, Ministry of Agriculture of People's Republic of China, Beijing 100025, China
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Digital PCR: What Relevance to Plant Studies? BIOLOGY 2020; 9:biology9120433. [PMID: 33266157 PMCID: PMC7760125 DOI: 10.3390/biology9120433] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023]
Abstract
Simple Summary Digital PCR is a third-generation technology based on the subdivision of the analytical sample into numerous partitions that are amplified individually. This review presents the major applications of digital PCR (dPCR) technology developed so far in the field of plant science. In greater detail, dPCR assays have been developed to trace genetically modified plant components, pathogenic and non-pathogenic microorganisms, and plant species. Other applications have concerned the study of the aspects of structural and functional genetics. Abstract Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.
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Abstract
DNA libraries are predisposed to template mispairing during conventional “bulk” PCR, leading to the loss of unique sequences. The latter is facilitated by the nonuniform distribution of templates frequently observed in DNA libraries. These effects result in a prominent reduction of the original diversity. The encapsulation of DNA repertoires in liquid droplets abolishes the effects of mispairing in DNA libraries. The fundamental advantages of emulsion PCR (ePCR) over bulk PCR are illustrated by deep sequencing and mathematical modeling, which provide the general strategy for ePCR rationalization. The quasi single-molecule ePCR reveals total genetic information by counteracting the degeneration of DNA libraries’ diversity. Conventional “bulk” PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases. Amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.
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Voegel TM, Larrabee MM, Nelson LM. Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil. Can J Microbiol 2020; 67:174-187. [PMID: 32910858 DOI: 10.1139/cjm-2020-0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH4+-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.
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Affiliation(s)
- Tanja M Voegel
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Melissa M Larrabee
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Louise M Nelson
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
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19
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Wang X, Chen Y, Chen X, Peng C, Wang L, Xu X, Wu J, Wei W, Xu J. A highly integrated system with rapid DNA extraction, recombinase polymerase amplification, and lateral flow biosensor for on-site detection of genetically modified crops. Anal Chim Acta 2020; 1109:158-168. [PMID: 32252899 DOI: 10.1016/j.aca.2020.02.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 01/29/2023]
Abstract
With the large-scale planting of genetically modified (GM) crops, the development of a rapid and convenient method for on-site monitoring GM crops is needed. In this study, a duplex recombinase polymerase amplification (DRPA)-based, quick and simple detection system is presented for on-site detection of GM crops. In this system, a rapid DNA extraction method, a DRPA, and a lateral flow biosensor (LFB) are integrated to allow for rapid DNA extraction and amplification, and fast visualization of the detection results. Using the rapid DNA extraction method, high-quality DNA suitable for RPA and polymerase chain reaction (PCR) was quickly isolated from various crops within 5 min. Utilizing the optimal DRPA assay, the universal screening sequences (Cauliflower mosaic virus 35S promoter [35S] and Agrobacterium tumefaciens NOS terminator [NOS]) were rapidly and simultaneously amplified with high selectivity and sensitivity. The sensitivity threshold of the DRPA assay was ∼10 copies for GM soybean genomic DNA and 100 ng DNA of 0.1% GM soybean. In combination with the LFB in an enclosed cassette, the entire detection process was performed in approximately 20-30 min and eliminated the carryover contamination. No special or expensive equipment was needed for the detection process. The system was successfully applied and validated for on-site detection of GM rice, demonstrating its suitability for on-site testing of GM crops and high potential for application to other fields, especially in low-resource regions that require rapid detection of DNA targets.
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Affiliation(s)
- Xiaofu Wang
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, 310021, China
| | - Yu Chen
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; College of Chemistry and Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Xiaoyun Chen
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Cheng Peng
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, 310021, China
| | - Liu Wang
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Wei Wei
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, 310021, China
| | - Junfeng Xu
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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20
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Singh M, Pal D, Sood P, Randhawa G. Loop-mediated isothermal amplification assays: Rapid and efficient diagnostics for genetically modified crops. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.106759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Cui X, Jin M, Zhang C, Du P, Chen G, Qin G, Jiang Z, Zhang Y, Li M, Liao Y, Wang Y, Cao Z, Yan F, Abd El-Aty AM, Wang J. Enhancing the Sensitivity of the Bio-barcode Immunoassay for Triazophos Detection Based on Nanoparticles and Droplet Digital Polymerase Chain Reaction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12936-12944. [PMID: 31670953 DOI: 10.1021/acs.jafc.9b05147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
An ultrasensitive bio-barcode competitive immunoassay method based on droplet digital polymerase chain reaction (ddPCR) was developed for the determination of triazophos. Gold nanoparticles (AuNPs) were coated with monoclonal antibodies (mAbs) and complementary double-stranded DNA (dsDNA), which included bio-barcode DNA and thiol-capped DNA. Magnetic nanoparticle (MNP) probes were constructed by modifying the MNPs with ovalbumin-hapten conjugates (OVA-hapten). The target pesticide and OVA-hapten on the surface of the MNP probes competed with the AuNP probes simultaneously, and then the bio-barcode DNA was released for quantification by ddPCR. The concentration of released DNA was inversely proportional to the concentration of pesticide to be tested. Under the optimum conditions, the competitive immunoassay exhibited a wide linear range of 0.01-20 ng/mL and a low detection limit of 0.002 ng/mL. Spike recovery tests were carried out using apple, rice, cabbage, and cucumber samples to verify the feasibility of the method. The recovery and relative standard deviations (RSDs) of the technique ranged from 76.9 to 94.4% and from 10.8 to 19.9%, respectively. To further validate the results, a linear correlation analysis was performed between the proposed method and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Consequently, the bio-barcode immunoassay based on nanoparticles and ddPCR, an ultrasensitive method, showed great potential for the determination of target pesticides in real samples.
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Affiliation(s)
- Xueyan Cui
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Chan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Pengfei Du
- Institute of Agro-Food Science and Technology , Shandong Academy of Agricultural Sciences , Jinan , Shandong 250100 , People's Republic of China
| | - Ge Chen
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Guoxin Qin
- Agro-Product Quality Safety and Testing Technology Research Institute , Guangxi Academy of Agricultural Sciences , Nanning , Guangxi 530007 , People's Republic of China
| | - Zejun Jiang
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Yudan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Mingjie Li
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Yun Liao
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Yuanshang Wang
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Zhen Cao
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
| | - Feiyan Yan
- Agro-Product Quality Safety and Testing Technology Research Institute , Guangxi Academy of Agricultural Sciences , Nanning , Guangxi 530007 , People's Republic of China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine , Cairo University , 12211 Giza , Egypt
- Department of Medical Pharmacology, Medical Faculty , Ataturk University , 25240 Erzurum , Turkey
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products , Chinese Academy of Agricultural Science , Beijing 100081 , People's Republic of China
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Bogožalec Košir A, Demšar T, Štebih D, Žel J, Milavec M. Digital PCR as an effective tool for GMO quantification in complex matrices. Food Chem 2019; 294:73-78. [PMID: 31126507 DOI: 10.1016/j.foodchem.2019.05.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
The increased use of genetically modified organisms (GMOs) is accompanied by increased complexity of the matrices that contain GMOs. The most common DNA-based approach for GMO detection and quantification is real-time quantitative polymerase chain reaction (qPCR). However, as qPCR is sensitive to inhibitors and relies on standard curves for quantification, it has limited application in GMO quantification for complex matrices. To overcome this hurdle in DNA quantification, we present droplet digital PCR (ddPCR) assays that were designed to target 'Roundup Ready' soybean and the soybean reference gene. Three ddPCR assays were transferred from qPCR to QX100/QX200 ddPCR platforms and characterised. Together, the fitness-for-purpose study on four real-life samples and the use of a chamber-based PCR system, showed that dPCR has great potential to improve such measurements in GMO testing and monitoring of food authenticity.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
| | - Tina Demšar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
| | - Dejan Štebih
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
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23
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Dupas E, Legendre B, Olivier V, Poliakoff F, Manceau C, Cunty A. Comparison of real-time PCR and droplet digital PCR for the detection of Xylella fastidiosa in plants. J Microbiol Methods 2019; 162:86-95. [DOI: 10.1016/j.mimet.2019.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 12/14/2022]
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24
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Droplet digital PCR applications in the tuberculosis world. Tuberculosis (Edinb) 2019; 117:85-92. [DOI: 10.1016/j.tube.2019.07.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/24/2019] [Accepted: 07/02/2019] [Indexed: 11/23/2022]
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25
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Cottenet G, Blancpain C, Chuah PF. Performance assessment of digital PCR for the quantification of GM-maize and GM-soya events. Anal Bioanal Chem 2019; 411:2461-2469. [PMID: 30810790 DOI: 10.1007/s00216-019-01692-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/28/2019] [Accepted: 02/13/2019] [Indexed: 11/25/2022]
Abstract
Accurate quantitative methods are needed to determine the amount of transgenic material in ingredients and comply with labelling GMO thresholds. Quantitative real-time PCR methods are usually applied for GMO quantification, but since a few years, digital PCR (dPCR) has been described as a potential alternative by quantifying DNA molecules directly without any standard curves. In this study, the performance of dPCR to quantify 9 GM-soya events and 15 GM-maize events was assessed. Following GMO validation guidelines, the trueness and precision were determined on high, medium and low levels of transgenic content. Results showed biases below ± 25% and satisfactory precision data. Limits of quantification were determined for each GM-event and were between 12 and 31 target copies. The reliability of GMO quantification by dPCR was further confirmed by analysing several proficiency test samples. Overall, dPCR showed accurate and precise GMO quantification on all the tested GM-events, from high to low transgenic amount. With its ease-of-use, dPCR was found to be an appealing alternative technology for routine GMO testing laboratories. Graphical abstract.
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Affiliation(s)
- Geoffrey Cottenet
- Institute of Food Safety & Analytical Sciences - Nestlé Research, Vers-chez-les-Blanc, 1000, Lausanne 26, Switzerland.
| | - Carine Blancpain
- Institute of Food Safety & Analytical Sciences - Nestlé Research, Vers-chez-les-Blanc, 1000, Lausanne 26, Switzerland
| | - Poh Fong Chuah
- Nestlé Quality Assurance Center, 29 Quality Road, Singapore, 618802, Singapore
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26
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Yang L, Yang Y, Jin W, Zhang X, Li X, Wu Y, Li J, Li L. Development and Interlaboratories Validation of Event-Specific Quantitative Real-Time PCR Method for Genetically Modified Rice G6H1 Event. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8179-8186. [PMID: 29985602 DOI: 10.1021/acs.jafc.8b01519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The transgenic rice G6H1 was a new event with the traits of herbicide-tolerance and insect-resistant. Herein, we developed one event-specific real-time PCR method with high specificity and sensitivity for G6H1 event quantitative analysis, and validated its performance on practical samples quantification through a collaborative ring trial. A total of eight laboratories participated in this validation and quantified three blind G6H1 powder samples including DNA extraction and real-time PCR analysis. The statistically analyzed results from returned data confirmed its high PCR efficiency and good linearity, trueness, and precision, indicating that the developed G6H1 real-time PCR assay was accurate, reliable, and comparable for G6H1 identification and quantification.
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Affiliation(s)
- Litao Yang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yu Yang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Wujun Jin
- Biotechnology Research Institute , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Xiujie Zhang
- Development Center of Science and Technology , Ministry of Agriculture of People's Republic of China , Beijing 100025 , China
| | - Xiaying Li
- Development Center of Science and Technology , Ministry of Agriculture of People's Republic of China , Beijing 100025 , China
| | - Yuhua Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute , Chinese Academy of Agricultural Sciences , No. 2 Xudong Second Road , Wuhan 430062 , People's Republic of China
| | - Jun Li
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute , Chinese Academy of Agricultural Sciences , No. 2 Xudong Second Road , Wuhan 430062 , People's Republic of China
| | - Liang Li
- Biotechnology Research Institute , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
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Dobnik D, Gruden K, Žel J, Bertheau Y, Holst-Jensen A, Bohanec M. Decision Support for the Comparative Evaluation and Selection of Analytical Methods: Detection of Genetically Modified Organisms as an Example. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1194-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Demeke T, Eng M. Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 15:24-29. [PMID: 29922591 PMCID: PMC6006385 DOI: 10.1016/j.bdq.2018.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/08/2018] [Accepted: 03/28/2018] [Indexed: 11/06/2022]
Abstract
Droplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantification of GE canola events by ddPCR. The suitability of four endogenous reference sequences (HMG-I/Y, FatA(A), CruA and Ccf) for absolute quantification of GE canola events by ddPCR was investigated. The effect of DNA extraction methods and DNA quality on the assessment of reference gene copy numbers was also investigated. ddPCR results were affected by the use of single vs. two copy reference genes. The single copy, FatA(A), reference gene was found to be stable and suitable for absolute quantification of GE canola events by ddPCR. For the copy numbers measured, the HMG-I/Y reference gene was less consistent than FatA(A) reference gene. The expected ddPCR values were underestimated when CruA and Ccf (two copy endogenous Cruciferin sequences) were used because of high number of copies. It is important to make an adjustment if two copy reference genes are used for ddPCR in order to obtain accurate results. On the other hand, real-time quantitative PCR results were not affected by the use of single vs. two copy reference genes.
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Key Words
- Canola
- Ccf, Cruciferin
- CruA, Cruciferin A
- DMF, DNeasy® mericon Food kit
- DNA extraction
- Digital PCR
- FID, Fast ID Genomic DNA extraction kit
- FatA(A), Acyl-ACP thioesterase
- GE, genetically engineered
- GMO
- GMO, genetically modified organism
- GMQ2, GM Quicker II DNA extraction kit
- HMG-I/Y, high-mobility group protein
- NSF, NucleoSpin Food kit
- PCR, polymerase chain reaction
- Reference genes
- SNP, single nucleotide polymorphism
- dPCR, digital PCR
- ddPCR, droplet digital PCR
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Affiliation(s)
- Tigst Demeke
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, Canada
| | - Monika Eng
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, Canada
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Demeke T, Dobnik D. Critical assessment of digital PCR for the detection and quantification of genetically modified organisms. Anal Bioanal Chem 2018; 410:4039-4050. [PMID: 29574561 PMCID: PMC6010488 DOI: 10.1007/s00216-018-1010-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022]
Abstract
The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing. Graphical abstract There are generally three different options for absolute quantification of genetically modified organisms (GMOs) using digital PCR: droplet- or chamber-based and droplets in chambers. All have in common the distribution of reaction mixture into several partitions, which are all subjected to PCR and scored at the end-point as positive or negative. Based on these results GMO content can be calculated.
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Affiliation(s)
- Tigst Demeke
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, MB, R3C3G8, Canada
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
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Abstract
The standard-curve based simplex quantitative polymerase chain reaction (qPCR) has been the gold standard for DNA target quantification for more than a decade. The large and growing number of individual analyses needed to test for genetically modified organisms (GMOs) is reducing the cost-effectiveness of qPCR. Droplet digital PCR (ddPCR) enables absolute quantification without standard curves, avoids the amplification efficiency bias observed with qPCR, allows more accurate estimations at low target copy numbers and, in combination with multiplexing, significantly improves cost efficiency. Here we describe two protocols for multiplex quantification of GM maize events: (1) nondiscriminating, with multiplex quantification of targets as a group (12 GM maize lines) and (2) discriminating, with multiplex quantification of individual targets (events). The first enables the quantification of twelve European Union authorized GM maize events as a group with only two assays, but does not permit determination of the individual events present. The second protocol enables the quantification of four individual targets (three GM events and one endogene) in a single reaction. Both protocols can be modified for quantification of any other DNA target.
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31
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Dobnik D, Demšar T, Huber I, Gerdes L, Broeders S, Roosens N, Debode F, Berben G, Žel J. Inter-laboratory analysis of selected genetically modified plant reference materials with digital PCR. Anal Bioanal Chem 2018; 410:211-221. [PMID: 29071363 PMCID: PMC5748423 DOI: 10.1007/s00216-017-0711-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022]
Abstract
Digital PCR (dPCR), as a new technology in the field of genetically modified (GM) organism (GMO) testing, enables determination of absolute target copy numbers. The purpose of our study was to test the transferability of methods designed for quantitative PCR (qPCR) to dPCR and to carry out an inter-laboratory comparison of the performance of two different dPCR platforms when determining the absolute GM copy numbers and GM copy number ratio in reference materials certified for GM content in mass fraction. Overall results in terms of measured GM% were within acceptable variation limits for both tested dPCR systems. However, the determined absolute copy numbers for individual genes or events showed higher variability between laboratories in one third of the cases, most possibly due to variability in the technical work, droplet size variability, and analysis of the raw data. GMO quantification with dPCR and qPCR was comparable. As methods originally designed for qPCR performed well in dPCR systems, already validated qPCR assays can most generally be used for dPCR technology with the purpose of GMO detection. Graphical abstract The output of three different PCR-based platforms was assessed in an inter-laboratory comparison.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Tina Demšar
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority (LGL), Veterinärstraße 2, 85764, Oberschleißheim, Germany
| | - Lars Gerdes
- Bavarian Health and Food Safety Authority (LGL), Veterinärstraße 2, 85764, Oberschleißheim, Germany
| | - Sylvia Broeders
- Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy Roosens
- Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Frederic Debode
- Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030, Gembloux, Belgium
| | - Gilbert Berben
- Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030, Gembloux, Belgium
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia
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